Hierarchical Clustering

Hierarchical clustering is a machine learning technique used to group data points into clusters based on their similarities. It is a powerful algorithm that can help to discover hidden patterns and structures within a dataset. In this article, we will explore the concept of hierarchical clustering, its types, and how it can be implemented in Python.

What is Hierarchical Clustering?

Hierarchical clustering is a technique used to group similar objects into clusters. It is based on the principle of grouping similar objects together and then gradually merging them into larger and larger clusters until all objects are in a single cluster. The output of the hierarchical clustering algorithm is a dendrogram, which is a tree-like diagram that shows the hierarchical relationships between the clusters.

Types of Hierarchical Clustering

There are two main types of hierarchical clustering:

  1. Agglomerative clustering: This is a bottom-up approach where each data point is treated as a separate cluster and then merged together to form larger clusters.
  2. Divisive clustering: This is a top-down approach where all data points are treated as a single cluster and then divided recursively into smaller clusters.

How does Hierarchical Clustering Work?

Hierarchical clustering works by computing the distance between all pairs of data points and then merging the closest pair of clusters iteratively until all data points belong to a single cluster. The distance between two clusters can be computed using various distance metrics such as Euclidean distance, Manhattan distance, and Cosine similarity.

Implementing Hierarchical Clustering in Python

Python provides several libraries for implementing hierarchical clustering such as Scikit-learn, SciPy, and PyClustering. Here, we will use the Scikit-learn library to implement hierarchical clustering.

Step 1: Importing Libraries and Loading Data

import pandas as pd
import numpy as np
from sklearn.cluster import AgglomerativeClustering
from sklearn.preprocessing import StandardScaler

# Load data
data = pd.read_csv('data.csv')
X = data.iloc[:, [0, 1, 2]].values

Step 2: Preprocessing Data

Before applying hierarchical clustering, we need to preprocess the data by scaling it to have zero mean and unit variance. This is done to ensure that all variables contribute equally to the clustering process.

# Scale data
scaler = StandardScaler()
X_scaled = scaler.fit_transform(X)

Step 3: Applying Hierarchical Clustering

We will use the AgglomerativeClustering class from Scikit-learn to apply hierarchical clustering to our dataset. We will set the number of clusters to 3 and use the Ward linkage method, which minimizes the variance of the clusters being merged.

# Apply hierarchical clustering
hc = AgglomerativeClustering(n_clusters=3, linkage='ward')
y_hc = hc.fit_predict(X_scaled)

Step 4: Visualizing Clusters

We can visualize the clusters by plotting a scatter plot of the data points with different colors representing the different clusters.

import matplotlib.pyplot as plt

# Create scatter plot
plt.scatter(X_scaled[y_hc == 0, 0], X_scaled[y_hc == 0, 1], s=100, c='red', label='Cluster 1')
plt.scatter(X_scaled[y_hc == 1, 0], X_scaled[y_hc == 1, 1], s=100, c='blue', label='Cluster 2')
plt.scatter(X_scaled[y_hc == 2, 0], X_scaled[y_hc == 2, 1], s=100, c='green', label='Cluster 3')

# Add labels and title
plt.title('Hierarchical Clustering')

# Add legend

# Show plot

In the code above, we use boolean indexing to select the data points belonging to each cluster and plot them with a different color. We also add labels to the axes, a title to the plot, and a legend to identify the different clusters. Finally, we show the plot using the show() function.


Hierarchical clustering is a powerful technique that can help to uncover hidden structures within a dataset. It is a simple and intuitive algorithm that can be applied to a wide range of data types and sizes. In this article, we have explored the concept of hierarchical clustering, its types, and how it can be implemented in Python using the Scikit-learn library.

By following the steps outlined in this article, you can apply hierarchical clustering to your own dataset and visualize the resulting clusters. This can help to identify patterns and relationships within the data that may be useful for further analysis or decision-making.

If you want to learn more about hierarchical clustering or other machine learning techniques, there are many resources available online, including tutorials, courses, and books. By continuing to learn and explore new techniques, you can stay ahead of the curve and become a more proficient data scientist.

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